Somatic mutation detection and classification through probabilistic integration of clonal population information.
, 44 (2019)
Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.
, 4001 (2018)
Copy number signatures in ovarian cancer.
, 1208-1209 (2018)
Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.
, 2002 (2018)
Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.
TERT promoter mutation in adult granulosa cell tumor of the ovary.
Mod. Pathol. (2018)
Engineered in-vitro cell line mixtures and robust evaluation of computational methods for clonal decomposition and longitudinal dynamics in cancer.
, 13467 (2017)
LINE-1 retrotransposon-mediated DNA transductions in endometriosis associated ovarian cancers.
Gynecol. Oncol. (2017)
The driver landscape of sporadic chordoma.
, 890 (2017)
Prognostic Model to Predict Post-Autologous Stem-Cell Transplantation Outcomes in Classical Hodgkin Lymphoma.
J. Clin. Oncol. JCO2017727925 (2017)
ReMixT: clone-specific genomic structure estimation in cancer.
, 140 (2017)
Genetic and epigenetic inactivation of SESTRIN1 controls mTORC1 and response to EZH2 inhibition in follicular lymphoma.
Sci Transl Med
Kronos: a workflow assembler for genome analytics and informatics.
Observing Clonal Dynamics Across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer.
Cold Spring Harb Perspect Med (2017)
E-scape: interactive visualization of single-cell phylogenetics and cancer evolution.
, 549-550 (2017)
Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes.
, 856-865 (2017)
Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin-specific clinical impact.
, 2760-2770 (2017)
CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion.
Nucleic Acids Res.
, 6698-6716 (2017)
Enhancing knowledge discovery from cancer genomics data with Galaxy.
, 1-13 (2017)
ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data.
, 44 (2017)
CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.
, 7 (2017)
CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours.
, 14432 (2017)
Scalable whole-genome single-cell library preparation without preamplification.
, 167-173 (2017)
Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study.
, e1002197 (2016)
Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer.
Proc. Natl. Acad. Sci. U.S.A.
, 9967-76 (2016)
Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates.
Proc. Natl. Acad. Sci. U.S.A.
, 8484-9 (2016)
Clonal genotype and population structure inference from single-cell tumor sequencing.
, 573-6 (2016)
Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer.
, 758-67 (2016)
The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes.
, 11479 (2016)
densityCut: an efficient and versatile topological approach for automatic clustering of biological data.
, 2567-76 (2016)
Identification of the epigenetic reader CBX2 as a potential drug target in advanced prostate cancer.
, 16 (2016)
Synchronous Endometrial and Ovarian Carcinomas: Evidence of Clonality.
J. Natl. Cancer Inst.
, djv428 (2016)
Divergent clonal selection dominates medulloblastoma at recurrence.
, 351-7 (2016)
The genomic landscape of epithelioid sarcoma cell lines and tumours.
, 63-73 (2016)
Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.
, 8760 (2015)
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
, 8554 (2015)
Cell of origin of transformed follicular lymphoma.
, 2118-27 (2015)
Hereditary Diffuse Gastric Cancer Syndrome: CDH1 Mutations and Beyond.
, 23-32 (2015)
Using Somatic Mutations to Guide Treatment Decisions: Context Matters.
, 275-6 (2015)
Spatial genomic heterogeneity within localized, multifocal prostate cancer.
, 736-45 (2015)
Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.
, 84 (2015)
Recurrent genomic rearrangements in primary testicular lymphoma.
, 136-41 (2015)
Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden.
, 201-9 (2015)
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution.
, 422-6 (2015)
An RCOR1 loss-associated gene expression signature identifies a prognostically significant DLBCL subgroup.
, 959-66 (2015)
A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer.
, 115-27 (2015)
DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts.
, 5871 (2014)
Intratumoral heterogeneity in a minority of ovarian low-grade serous carcinomas.
, 982 (2014)
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.
, 1881-93 (2014)
Mutational context and diverse clonal development in early and late bladder cancer.
, 1649-63 (2014)
Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4.
, 427-9 (2014)
PyClone: statistical inference of clonal population structure in cancer.
, 396-8 (2014)
Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma.
, 329-35 (2014)
Genomic rearrangements involving programmed death ligands are recurrent in primary mediastinal large B-cell lymphoma.
, 2062-5 (2014)
Ovarian and endometrial endometrioid carcinomas have distinct CTNNB1 and PTEN mutation profiles.
, 128-34 (2014)
A robust hidden semi-Markov model with application to aCGH data processing.
Int J Data Min Bioinform
, 427-42 (2013)
Type-specific cell line models for type-specific ovarian cancer research.
, e72162 (2013)
Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling.
, 21-34 (2013)
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing.
, 1256-65 (2013)
Distinguishing somatic and germline copy number events in cancer patient DNA hybridized to whole-genome SNP genotyping arrays.
Methods Mol. Biol.
, 355-72 (2013)
iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data.
, 519-29 (2013)
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
, R124 (2012)
Gene expression profiling of microdissected Hodgkin Reed-Sternberg cells correlates with treatment outcome in classical Hodgkin lymphoma.
, 3530-40 (2012)
Mutation discovery in regions of segmental cancer genome amplifications with CoNAn-SNV: a mixture model for next generation sequencing of tumors.
, e41551 (2012)
nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.
, 2250-61 (2012)
Use of mutation profiles to refine the classification of endometrial carcinomas.
, 20-30 (2012)
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer.
, 1995-2007 (2012)
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
, 346-52 (2012)
The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
, 395-9 (2012)
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
, 907-13 (2012)
BRCA1 and BRCA2 mutations correlate with TP53 abnormalities and presence of immune cell infiltrates in ovarian high-grade serous carcinoma.
, 740-50 (2012)
14-3-3 fusion oncogenes in high-grade endometrial stromal sarcoma.
Proc. Natl. Acad. Sci. U.S.A.
, 929-34 (2012)
Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers.
N. Engl. J. Med.
, 234-42 (2012)
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data.
, 167-75 (2012)
Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities.
, 12-8 (2011)
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
PLoS Comput. Biol.
, e1001138 (2011)
Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data.
, 1481-8 (2011)
Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas.
, 567-73 (2011)
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers.
, 377-81 (2011)
ARID1A mutations in endometriosis-associated ovarian carcinomas.
N. Engl. J. Med.
, 1532-43 (2010)
Acquired TNFRSF14 mutations in follicular lymphoma are associated with worse prognosis.
, 9166-74 (2010)
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors.
, R82 (2010)
High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes.
Genes Chromosomes Cancer
, 669-81 (2010)
Genome-wide copy number analysis of Hodgkin Reed-Sternberg cells identifies recurrent imbalances with correlations to treatment outcome.
, 418-27 (2010)
Tumor-associated macrophages and survival in classic Hodgkin's lymphoma.
N. Engl. J. Med.
, 875-85 (2010)
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
, 730-6 (2010)
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin.
, 181-5 (2010)
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.
, 809-13 (2009)
Mutation of FOXL2 in granulosa-cell tumors of the ovary.
N. Engl. J. Med.
, 2719-29 (2009)
Model-based clustering of array CGH data.
, i30-8 (2009)
Genome-wide profiling of follicular lymphoma by array comparative genomic hybridization reveals prognostically significant DNA copy number imbalances.
, 137-48 (2009)
Modeling recurrent DNA copy number alterations in array CGH data.
, i450-8 (2007)
Integrating copy number polymorphisms into array CGH analysis using a robust HMM.
, e431-9 (2006)
Ulysses - an application for the projection of molecular interactions across species.
, R106 (2005)
Atlas - a data warehouse for integrative bioinformatics.
, 34 (2005)
Pegasys: software for executing and integrating analyses of biological sequences.
, 40 (2004)
GeneComber: combining outputs of gene prediction programs for improved results.
, 1296-7 (2003)